Metagenome Normalization and Feature Selection

Load Libraries

Code

##################
# LOAD LIBRARIES #
##################
library(tidyverse)
library(mixOmics) 
library(readxl)
library(cowplot)
library(RColorBrewer)
library(scales)
select <- dplyr::select
map <- purrr::map

# setwd("/Users/vilkal/work/Brolidens_work/Projects/Candida-omics/src")

taxonomy <- c(
  "kingdom",
  "phylum",
  "class",
  "order",
  "family",
  "genus",
  "species",
  "strain"
)

The first part of this script follows the preprocessing steps outlined on the MixOmics tutorial https://mixomics.org/mixmc/mixmc-preprocessing/

data_path <- "/Users/vilkal/work/Brolidens_work/Projects/Candida-omics/Tidy_data/Metagenomics/Metageonome_all_vagswab_metaphlan.csv"
meta_path <- "/Users/vilkal/Downloads/Metadata_svamp.xlsx"

#############
# LOAD DATA #
#############
data <- read_csv(data_path) 

Rows: 682 Columns: 170
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr   (1): clade_name
dbl (169): zymomock_ex_1, neg_ex_1, neg_ex_2, zymomock_ex_2, neg_ex, zymomoc...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

meta_data <- read_xlsx(meta_path, sheet = "Metadata", skip = 1)

gr_data <- meta_data %>%
    rename(`Symptom score (0-5)` = "Symptom score (0-5) - ibland har de svarat olika skriftligt i frågeformuläret och muntligt vid inklusiion, då har jag valt den högsta scoren") %>%
  select(
    svamp_ID,
    `Fungal culture: C. albicans (y/n)`,
    `Fungal culture: Non-albicans candida spp. (y/n)`,
    `Symptom score (0-5)`,
    `Recurring fungal infections > 2/year (y/n)`
  ) %>%
    mutate(
  group = case_when(
    `Fungal culture: C. albicans (y/n)` == "1" &
      `Symptom score (0-5)` >= 1 &
      `Recurring fungal infections > 2/year (y/n)` == "1" ~
      "RVVCpos",

    `Fungal culture: C. albicans (y/n)` == "0" &
      `Recurring fungal infections > 2/year (y/n)` == "1" ~
      "RVVCneg",

    `Fungal culture: C. albicans (y/n)` == "1" &
      `Symptom score (0-5)` == 0 ~
      "AS",

    `Fungal culture: C. albicans (y/n)` == "0" &
      `Recurring fungal infections > 2/year (y/n)` == "0" ~
      "Control",

    `Fungal culture: C. albicans (y/n)` == "1" &
      `Recurring fungal infections > 2/year (y/n)` == "0" ~
      "Candidapos",

    TRUE ~ NA_character_
  )
) %>%
  select("svamp_ID", group, everything())

Step 2: Pre-filtering

keep taxa with at least 0.005% in at least 6% (2 out of 34) of samples, or at least 2% relative abundance in at least 1 sample.

# final
############################
# IDENTIFY TAXA TO FILTER #
###########################
t <- set_names(taxonomy, seq_along(taxonomy))
data <- data %>%
    select( -contains("ex"), -contains("seq"), -contains("_run2")) %>% # removes ctrl and extra samples
    select(-matches("_1W|_3M|_6M")) %>%
    mutate(
        level = factor(
            t[as.character(str_count(clade_name, "\\|") + 1)],
            levels = taxonomy),
            .after = "clade_name"
            ) 

n_samples <- select(data, starts_with("S")) %>% ncol() # number of good samples

# keep taxa with at least 0.005% in at least 6% (5 out of 84) of samples, or at least 2% relative abundance in at least 1 sample.

# Step 1. split clade name into seperate columns
temp <- data %>%
    separate(
    col = clade_name,
    into = taxonomy,
    sep = "\\|",
    #remove = FALSE,
    fill = "right"
  ) %>%
  # keeps any row where at least one numeric column has a value greater than zero
  filter(if_any(where(is.double), ~ .x > 0))

# Step 2. Identify the strains to remove
strains_to_remove <- temp %>%
  filter(level == "strain") %>%
  filter(
    !(rowSums(across(where(is.double), ~ .x > 0.005)) >=
      round(0.06 * n_samples) |
      rowSums(across(where(is.double), ~ .x >= 2)) >= 1)
  )

# pander table of strains to remove
strains_to_remove %>%
  arrange(desc(rowSums(across(where(is.numeric))))) %>%
  # removes samples with colsum = zero:
  select(
    -where(~ is.numeric(.x) && sum(.x) == 0)
  ) %>%
  knitr::kable(., digits = 1)

kingdom	phylum	class	order	family	genus	species	strain	level	KX64	S02	S03	S04	S05	S09	S14	S17	S18	S20	S22	S23	S24	S25	S27	S29	S30	S31	S32	S35	S37	S38	S39	S43	S44	S46	S47	S49	S52	S53	S54	S55	S60	S61	S62	S64_BL	S66_BL	S67_BL	S69_BL	S70_BL	S75_BL	S76_BL	S79_BL	S81_BL	S83_BL	S84_BL	S85_BL	S86_BL	S87_BL	S89_BL	S90_BL
k__Bacteria	p__Actinobacteria	c__Actinomycetia	o__Bifidobacteriales	f__Bifidobacteriaceae	g__Bifidobacterium	s__Bifidobacterium_bifidum	t__SGB17256	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.7	0.0	0.0	0	0.0	0	0.0	0.0	0	0.1	0.0	0	0.9	1.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Clostridia	o__Eubacteriales	f__Peptostreptococcaceae	g__Peptostreptococcus	s__Peptostreptococcus_anaerobius	t__SGB746	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.7	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	1.7	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Bacilli	o__Lactobacillales	f__Lactobacillaceae	g__Limosilactobacillus	s__Limosilactobacillus_coleohominis	t__SGB7100	strain	0.1	0.0	0.0	0	0.0	0	0.4	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.3	1.0
k__Bacteria	p__Firmicutes	c__Tissierellia	o__Tissierellales	f__Peptoniphilaceae	g__Peptoniphilus	s__Peptoniphilus_vaginalis	t__SGB6696	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	1.3	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.3	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Eukaryota	p__Ascomycota	c__Saccharomycetes	o__Saccharomycetales	f__Debaryomycetaceae	g__Candida	s__Candida_parapsilosis	t__EUK5480	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	1.1	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Actinomycetia	o__Actinomycetales	f__Actinomycetaceae	g__Mobiluncus	s__Mobiluncus_curtisii	t__SGB15487	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.1	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	1.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Bacteroidota	c__Bacteroidia	o__Bacteroidales	f__Prevotellaceae	g__Prevotella	s__Prevotella_sp_S7_1_8	t__SGB1501	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	1.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Bacilli	o__Lactobacillales	f__Lactobacillaceae	g__Limosilactobacillus	s__Limosilactobacillus_vaginalis	t__SGB7098	strain	0.0	0.7	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.2	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Coriobacteriia	o__Coriobacteriales	f__Atopobiaceae	g__Lancefieldella	s__Lancefieldella_rimae	t__SGB985	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.9	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Bacilli	o__Lactobacillales	f__Lactobacillaceae	g__Lacticaseibacillus	s__Lacticaseibacillus_paracasei	t__SGB7142	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.3	0.0	0.4	0.0	0.0
k__Bacteria	p__Firmicutes	c__Bacilli	o__Lactobacillales	f__Streptococcaceae	g__Streptococcus	s__Streptococcus_salivarius	t__SGB8007_group	strain	0.0	0.0	0.1	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.6	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Bacteroidota	c__Bacteroidia	o__Bacteroidales	f__Bacteroidales_unclassified	g__Bacteroidales_unclassified	s__Bacteroidales_bacterium_KA00251	t__SGB3324	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.6	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Tissierellia	o__Tissierellales	f__Peptoniphilaceae	g__Anaerococcus	s__Anaerococcus_vaginalis	t__SGB29499	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.2	0	0	0.4	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Bacteroidota	c__Bacteroidia	o__Bacteroidales	f__Prevotellaceae	g__Prevotella	s__Prevotella_veroralis	t__SGB1541	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.5	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Actinomycetia	o__Bifidobacteriales	f__Bifidobacteriaceae	g__Bifidobacterium	s__Bifidobacterium_longum	t__SGB17248	strain	0.0	0.0	0.0	0	0.2	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.3	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Proteobacteria	c__Gammaproteobacteria	o__Enterobacterales	f__Enterobacteriaceae	g__Escherichia	s__Escherichia_coli	t__SGB10068	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.5	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.1	0.0
k__Bacteria	p__Bacteroidota	c__Bacteroidia	o__Bacteroidales	f__Muribaculaceae	g__GGB1460	s__GGB1460_SGB2023	t__SGB2023	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.2	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.1	0	0.0	0.0	0.0	0	0.0	0	0	0	0.2	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Actinomycetia	o__Actinomycetales	f__Actinomycetaceae	g__Winkia	s__Winkia_neuii	t__SGB17191	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.4	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Bacilli	o__Bacillales	f__Staphylococcaceae	g__Staphylococcus	s__Staphylococcus_hominis	t__SGB7858	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.4	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Coriobacteriia	o__Eggerthellales	f__Eggerthellaceae	g__Cryptobacterium	s__Cryptobacterium_curtum	t__SGB962	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.4	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Coriobacteriia	o__Coriobacteriales	f__Atopobiaceae	g__Lancefieldella	s__Lancefieldella_parvula	t__SGB966	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.1	0	0.0	0.0	0	0	0	0.0	0	0	0.2	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Actinomycetia	o__Bifidobacteriales	f__Bifidobacteriaceae	g__Gardnerella	s__Gardnerella_vaginalis	t__SGB21500	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.3	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Bacteroidota	c__Bacteroidia	o__Bacteroidales	f__Prevotellaceae	g__Prevotella	s__Prevotella_corporis	t__SGB1504	strain	0.0	0.0	0.0	0	0.0	0	0.1	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.2	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Bacteroidota	c__Bacteroidia	o__Bacteroidales	f__Prevotellaceae	g__Prevotella	s__Prevotella_buccalis	t__SGB1514	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.2	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.1	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Bacteroidota	c__Bacteroidia	o__Bacteroidales	f__Prevotellaceae	g__Prevotella	s__Prevotella_melaninogenica	t__SGB1547	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.3	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Actinomycetia	o__Actinomycetales	f__Actinomycetaceae	g__Arcanobacterium	s__Arcanobacterium_sp_S3PF19	t__SGB17200	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.3	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Bacteroidota	c__Bacteroidia	o__Bacteroidales	f__Prevotellaceae	g__GGB1144	s__GGB1144_SGB1468	t__SGB1468	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.3	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Proteobacteria	c__Gammaproteobacteria	o__Pasteurellales	f__Pasteurellaceae	g__Haemophilus	s__Haemophilus_haemolyticus	t__SGB9649	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.2	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Tissierellia	o__Tissierellales	f__Peptoniphilaceae	g__Peptoniphilus	s__Peptoniphilus_duerdenii	t__SGB6715	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.2	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Clostridia	o__Eubacteriales	f__Peptococcaceae	g__Peptococcus	s__Peptococcus_niger	t__SGB4050	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.2	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Bacilli	o__Lactobacillales	f__Streptococcaceae	g__Streptococcus	s__Streptococcus_mitis	t__SGB8185	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.1	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.1	0.0	0.0	0.0
k__Bacteria	p__Bacteroidota	c__Bacteroidia	o__Bacteroidales	f__Prevotellaceae	g__Prevotella	s__Prevotella_bergensis	t__SGB1505	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.1	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.1	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Tissierellia	o__Tissierellales	f__Peptoniphilaceae	g__Peptoniphilus	s__Peptoniphilus_gorbachii	t__SGB6699	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.2	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Tissierellia	o__Tissierellales	f__Peptoniphilaceae	g__Anaerococcus	s__Anaerococcus_jeddahensis	t__SGB6665	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.1	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Tissierellia	o__Tissierellales	f__Peptoniphilaceae	g__Anaerococcus	s__Anaerococcus_hydrogenalis	t__SGB6663	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.1	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Negativicutes	o__Veillonellales	f__Veillonellaceae	g__Veillonella	s__Veillonella_atypica	t__SGB6936	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.1	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Actinomycetia	o__Corynebacteriales	f__Corynebacteriaceae	g__Corynebacterium	s__Corynebacterium_glucuronolyticum	t__SGB17030	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.1
k__Bacteria	p__Bacteroidota	c__Bacteroidia	o__Bacteroidales	f__Prevotellaceae	g__Prevotella	s__Prevotella_buccalis	t__SGB1517_group	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.1	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Actinomycetia	o__Actinomycetales	f__Actinomycetaceae	g__Actinotignum	s__Actinotignum_sanguinis	t__SGB33732	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.1	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Actinomycetia	o__Actinomycetales	f__Actinomycetaceae	g__Actinomyces	s__Actinomyces_SGB17132	t__SGB17132_group	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.1	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Bacilli	o__Bacillales	f__Staphylococcaceae	g__Staphylococcus	s__Staphylococcus_epidermidis	t__SGB7865	strain	0.0	0.1	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Eukaryota	p__Ascomycota	c__Saccharomycetes	o__Saccharomycetales	f__Debaryomycetaceae	g__Candida	s__Candida_dubliniensis	t__EUK42374	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.1	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Coriobacteriia	o__Eggerthellales	f__Eggerthellaceae	g__Slackia	s__Slackia_exigua	t__SGB14784	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.1	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Clostridia	o__Eubacteriales	f__Oscillospiraceae	g__Mageeibacillus	s__Mageeibacillus_indolicus	t__SGB4002	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.1	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Actinomycetia	o__Actinomycetales	f__Actinomycetaceae	g__Mobiluncus	s__Mobiluncus_mulieris	t__SGB15486	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.1	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Actinomycetia	o__Actinomycetales	f__Actinomycetaceae	g__Schaalia	s__Schaalia_turicensis	t__SGB17195	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.1	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Clostridia	o__Eubacteriales	f__Eubacteriales_unclassified	g__Fenollaria	s__Fenollaria_massiliensis	t__SGB6716	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.1	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Actinomycetia	o__Corynebacteriales	f__Corynebacteriaceae	g__Corynebacterium	s__Corynebacterium_amycolatum	t__SGB17036	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.1	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Actinomycetia	o__Corynebacteriales	f__Corynebacteriaceae	g__Corynebacterium	s__Corynebacterium_aurimucosum	t__SGB17102	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.1	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Proteobacteria	c__Gammaproteobacteria	o__Enterobacterales	f__Enterobacteriaceae	g__Salmonella	s__Salmonella_enterica	t__SGB10073	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Bacilli	o__Lactobacillales	f__Streptococcaceae	g__Streptococcus	s__Streptococcus_mitis	t__SGB8168	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Actinomycetia	o__Corynebacteriales	f__Corynebacteriaceae	g__Corynebacterium	s__Corynebacterium_tuscaniense	t__SGB17076	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Clostridia	o__Eubacteriales	f__Lachnospiraceae	g__Lachnospiraceae_unclassified	s__Lachnospiraceae_bacterium	t__SGB5267	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Actinomycetia	o__Corynebacteriales	f__Lawsonellaceae	g__Lawsonella	s__Lawsonella_SGB3665	t__SGB3665	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Bacteroidota	c__Bacteroidia	o__Bacteroidales	f__Prevotellaceae	g__Prevotella	s__Prevotella_vespertina	t__SGB1542	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Clostridia	o__Eubacteriales	f__Eubacteriales_unclassified	g__Eubacteriales_unclassified	s__Clostridiales_bacterium_KA00274	t__SGB7884	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Bacteroidota	c__Bacteroidia	o__Bacteroidales	f__Prevotellaceae	g__Prevotella	s__Prevotella_pallens	t__SGB1564	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Clostridia	o__Eubacteriales	f__Clostridiaceae	g__Clostridium	s__Clostridium_massiliamazoniense	t__SGB29082	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Actinomycetia	o__Corynebacteriales	f__Corynebacteriaceae	g__GGB10524	s__GGB10524_SGB17049	t__SGB17049	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Coriobacteriia	o__Eggerthellales	f__Eggerthellaceae	g__Gordonibacter	s__Gordonibacter_sp_Marseille_P4307	t__SGB14790	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Tissierellia	o__Tissierellales	f__Peptoniphilaceae	g__Anaerococcus	s__Anaerococcus_prevotii	t__SGB6676	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Tissierellia	o__Tissierellales	f__Peptoniphilaceae	g__Parvimonas	s__Parvimonas_parva	t__SGB6648	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Tenericutes	c__Tenericutes_unclassified	o__Mycoplasmoidales	f__Metamycoplasmataceae	g__Metamycoplasma	s__Metamycoplasma_hominis	t__SGB5926	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Bacilli	o__Bacillales	f__Listeriaceae	g__Listeria	s__Listeria_monocytogenes	t__SGB7535	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Actinomycetia	o__Propionibacteriales	f__Propionibacteriaceae	g__Propionimicrobium	s__Propionimicrobium_lymphophilum	t__SGB15491	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Actinomycetia	o__Corynebacteriales	f__Corynebacteriaceae	g__Corynebacterium	s__Corynebacterium_aurimucosum	t__SGB17109	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Bacteroidota	c__Bacteroidia	o__Bacteroidales	f__Prevotellaceae	g__Prevotella	s__Prevotella_jejuni	t__SGB1545	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Proteobacteria	c__Betaproteobacteria	o__Burkholderiales	f__Sutterellaceae	g__GGB36599	s__GGB36599_SGB9269	t__SGB9269	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Actinomycetia	o__Actinomycetales	f__Actinomycetaceae	g__Varibaculum	s__Varibaculum_cambriense	t__SGB15482	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Tissierellia	o__Tissierellales	f__Peptoniphilaceae	g__Finegoldia	s__Finegoldia_magna	t__SGB6686_group	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Coriobacteriia	o__Coriobacteriales	f__Atopobiaceae	g__Atopobium	s__Atopobium_minutum	t__SGB987	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Tissierellia	o__Tissierellales	f__Peptoniphilaceae	g__Urinicoccus	s__Urinicoccus_massiliensis	t__SGB29501	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Clostridia	o__Eubacteriales	f__Eubacteriales_unclassified	g__Levyella	s__Levyella_massiliensis	t__SGB5300	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Proteobacteria	c__Gammaproteobacteria	o__Pseudomonadales	f__Pseudomonadaceae	g__Pseudomonas	s__Pseudomonas_aeruginosa	t__SGB12320	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Proteobacteria	c__Gammaproteobacteria	o__Pasteurellales	f__Pasteurellaceae	g__Haemophilus	s__Haemophilus_parainfluenzae	t__SGB9712	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Tissierellia	o__Tissierellia_unclassified	f__Tissierellia_unclassified	g__Ezakiella	s__Ezakiella_coagulans	t__SGB6728	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Clostridia	o__Eubacteriales	f__Lachnospiraceae	g__GGB3883	s__GGB3883_SGB5265	t__SGB5265	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Actinomycetia	o__Actinomycetales	f__Actinomycetaceae	g__Actinotignum	s__Actinotignum_timonense	t__SGB17174	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Proteobacteria	c__Gammaproteobacteria	o__Pasteurellales	f__Pasteurellaceae	g__Mannheimia	s__Mannheimia_massilioguelmaensis	t__SGB9743	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Bacilli	o__Lactobacillales	f__Streptococcaceae	g__Streptococcus	s__Streptococcus_parasanguinis	t__SGB8071	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Actinomycetia	o__Propionibacteriales	f__Propionibacteriaceae	g__Cutibacterium	s__Cutibacterium_acnes	t__SGB16955	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Proteobacteria	c__Betaproteobacteria	o__Neisseriales	f__Neisseriaceae	g__Neisseria	s__Neisseria_subflava	t__SGB9450_group	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Synergistetes	c__Synergistia	o__Synergistales	f__Synergistaceae	g__Jonquetella	s__Jonquetella_anthropi	t__SGB15495	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Bacteroidota	c__Bacteroidia	o__Bacteroidales	f__Porphyromonadaceae	g__Porphyromonas	s__Porphyromonas_uenonis	t__SGB1974	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Actinomycetia	o__Micrococcales	f__Brevibacteriaceae	g__Brevibacterium	s__Brevibacterium_sp_HMSC063G07	t__SGB23941	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Actinomycetia	o__Propionibacteriales	f__Propionibacteriaceae	g__Vaginimicrobium	s__Vaginimicrobium_propionicum	t__SGB33673	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Actinomycetia	o__Actinomycetales	f__Actinomycetaceae	g__Actinotignum	s__Actinotignum_urinale	t__SGB17176	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Negativicutes	o__Veillonellales	f__Veillonellaceae	g__Megasphaera	s__Megasphaera_micronuciformis	t__SGB5868	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Actinomycetia	o__Actinomycetales	f__Actinomycetaceae	g__Actinomyces	s__Actinomyces_sp_ph3	t__SGB17137_group	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Bacilli	o__Lactobacillales	f__Streptococcaceae	g__Streptococcus	s__Streptococcus_oralis	t__SGB8130	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Bacteroidota	c__Bacteroidia	o__Bacteroidales	f__Prevotellaceae	g__Prevotella	s__Prevotella_histicola	t__SGB1543	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Bacilli	o__Lactobacillales	f__Streptococcaceae	g__Streptococcus	s__Streptococcus_gordonii	t__SGB8053	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Erysipelotrichia	o__Erysipelotrichales	f__Erysipelotrichaceae	g__Bulleidia	s__Bulleidia_extructa	t__SGB6820	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Actinomycetia	o__Actinomycetales	f__Actinomycetaceae	g__Actinomyces	s__Actinomyces_sp_HMSC065F12	t__SGB17194	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Negativicutes	o__Veillonellales	f__Veillonellaceae	g__Veillonella	s__Veillonella_parvula	t__SGB6939	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Negativicutes	o__Veillonellales	f__Veillonellaceae	g__Veillonella	s__Veillonella_dispar	t__SGB6952	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Bacilli	o__Bacillales	f__Bacillales_unclassified	g__Gemella	s__Gemella_haemolysans	t__SGB7285_group	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Negativicutes	o__Veillonellales	f__Veillonellaceae	g__Dialister	s__Dialister_pneumosintes	t__SGB5842	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Coriobacteriia	o__Coriobacteriales	f__Coriobacteriaceae	g__Senegalimassilia	s__Senegalimassilia_anaerobia	t__SGB14824_group	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Actinomycetia	o__Micrococcales	f__Micrococcaceae	g__Rothia	s__Rothia_mucilaginosa	t__SGB16971_group	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Actinomycetia	o__Corynebacteriales	f__Corynebacteriaceae	g__Corynebacterium	s__Corynebacterium_uberis	t__SGB110762	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__CFGB1705	o__OFGB1705	f__FGB1705	g__GGB4260	s__GGB4260_SGB5794	t__SGB5794	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Actinomycetia	o__Bifidobacteriales	f__Bifidobacteriaceae	g__Bifidobacteriaceae_unclassified	s__Bifidobacteriaceae_bacterium_NR047	t__SGB33639	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Tissierellia	o__Tissierellales	f__Peptoniphilaceae	g__Anaerococcus	s__Anaerococcus_senegalensis	t__SGB6664	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Bacteroidota	c__Bacteroidia	o__Bacteroidales	f__Prevotellaceae	g__Prevotella	s__Prevotella_nigrescens	t__SGB1561	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Bacilli	o__Lactobacillales	f__Streptococcaceae	g__Streptococcus	s__Streptococcus_intermedius	t__SGB8025	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Negativicutes	o__Veillonellales	f__Veillonellaceae	g__Veillonella	s__Veillonella_rogosae	t__SGB6956	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Bacteroidota	c__Bacteroidia	o__Bacteroidales	f__Prevotellaceae	g__GGB1144	s__GGB1144_SGB1469	t__SGB1469	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Bacteroidota	c__Bacteroidia	o__Bacteroidales	f__Prevotellaceae	g__Prevotella	s__Prevotella_oris	t__SGB1525	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Erysipelotrichia	o__Erysipelotrichales	f__Erysipelotrichaceae	g__Solobacterium	s__Solobacterium_SGB6829	t__SGB6829	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Eukaryota	p__Ascomycota	c__Saccharomycetes	o__Saccharomycetales	f__Saccharomycetaceae	g__Nakaseomyces	s__Candida_glabrata	t__EUK5478	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Bacilli	o__Lactobacillales	f__Carnobacteriaceae	g__Granulicatella	s__Granulicatella_SGB8239	t__SGB8239_group	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Actinomycetia	o__Corynebacteriales	f__Corynebacteriaceae	g__Corynebacterium	s__Corynebacterium_simulans	t__SGB17120	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Clostridia	o__Eubacteriales	f__Eubacteriales_Family_XIII_Incertae_Sedis	g__Mogibacterium	s__Mogibacterium_diversum	t__SGB3922_group	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Bacilli	o__Lactobacillales	f__Carnobacteriaceae	g__Granulicatella	s__Granulicatella_adiacens	t__SGB8249	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Clostridia	o__Eubacteriales	f__Peptostreptococcaceae	g__Peptostreptococcus	s__Peptostreptococcus_sp_MV1	t__SGB747	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Bacilli	o__Lactobacillales	f__Streptococcaceae	g__Streptococcus	s__Streptococcus_australis	t__SGB8059_group	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Bacilli	o__Lactobacillales	f__Streptococcaceae	g__Streptococcus	s__Streptococcus_constellatus	t__SGB8026	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Tissierellia	o__Tissierellales	f__Peptoniphilaceae	g__Peptoniphilus	s__Peptoniphilus_grossensis	t__SGB6701	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Tissierellia	o__Tissierellales	f__Peptoniphilaceae	g__Anaerococcus	s__Anaerococcus_sp_Marseille_P3915	t__SGB29506	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Actinomycetia	o__Actinomycetales	f__Actinomycetaceae	g__Actinomyces	s__Actinomyces_urogenitalis	t__SGB15868	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Erysipelotrichia	o__Erysipelotrichales	f__Erysipelotrichaceae	g__Solobacterium	s__Solobacterium_moorei	t__SGB6826	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Actinomycetia	o__Actinomycetales	f__Actinomycetaceae	g__Mobiluncus	s__Mobiluncus_SGB15488	t__SGB15488	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Proteobacteria	c__Epsilonproteobacteria	o__Campylobacterales	f__Campylobacteraceae	g__Campylobacter	s__Campylobacter_concisus	t__SGB19351	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Tissierellia	o__Tissierellales	f__Peptoniphilaceae	g__Peptoniphilus	s__Peptoniphilus_urinimassiliensis	t__SGB6736	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Coriobacteriia	o__Coriobacteriales	f__Atopobiaceae	g__Lancefieldella	s__Lancefieldella_parvula	t__SGB964	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Actinomycetia	o__Actinomycetales	f__Actinomycetaceae	g__Schaalia	s__Schaalia_SGB17158	t__SGB17158_group	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Tissierellia	o__Tissierellales	f__Peptoniphilaceae	g__Anaerococcus	s__Anaerococcus_murdochii	t__SGB6671	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Actinomycetia	o__Micrococcales	f__Micrococcaceae	g__Rothia	s__Rothia_mucilaginosa	t__SGB16986	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Tissierellia	o__Tissierellales	f__Peptoniphilaceae	g__Peptoniphilus	s__Peptoniphilus_rachelemmaiella	t__SGB109696	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Actinomycetia	o__Actinomycetales	f__Actinomycetaceae	g__Actinobaculum	s__Actinobaculum_massiliense	t__SGB17172	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Bacteroidota	c__Bacteroidia	o__Bacteroidales	f__Prevotellaceae	g__Prevotella	s__Prevotella_salivae	t__SGB1522	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Bacteroidota	c__Bacteroidia	o__Bacteroidales	f__Prevotellaceae	g__Prevotella	s__Prevotella_baroniae	t__SGB1533	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Tissierellia	o__Tissierellales	f__Peptoniphilaceae	g__Anaerococcus	s__Anaerococcus_prevotii	t__SGB6679	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Tissierellia	o__Tissierellales	f__Peptoniphilaceae	g__Peptoniphilus	s__Peptoniphilus_sp_BV3C26	t__SGB6713	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Fusobacteria	c__Fusobacteriia	o__Fusobacteriales	f__Fusobacteriaceae	g__Fusobacterium	s__Fusobacterium_periodonticum	t__SGB5989_group	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Fusobacteria	c__Fusobacteriia	o__Fusobacteriales	f__Fusobacteriaceae	g__Fusobacterium	s__Fusobacterium_gonidiaformans	t__SGB5985	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Actinomycetia	o__Actinomycetales	f__Actinomycetaceae	g__Schaalia	s__Schaalia_SGB17168	t__SGB17168	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Actinomycetia	o__Propionibacteriales	f__Propionibacteriaceae	g__Cutibacterium	s__Cutibacterium_avidum	t__SGB16953	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Actinomycetia	o__Actinomycetales	f__Actinomycetaceae	g__Actinomyces	s__Actinomyces_graevenitzii	t__SGB17130_group	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Bacteroidota	c__Bacteroidia	o__Bacteroidales	f__Porphyromonadaceae	g__Porphyromonas	s__Porphyromonas_bobii	t__SGB2043	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Coriobacteriia	o__Coriobacteriales	f__Coriobacteriaceae	g__Olegusella	s__Olegusella_massiliensis	t__SGB960	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Actinomycetia	o__Corynebacteriales	f__Corynebacteriaceae	g__Corynebacterium	s__Corynebacterium_atypicum	t__SGB17094	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Tissierellia	o__Tissierellales	f__Peptoniphilaceae	g__Peptoniphilus	s__Peptoniphilus_harei	t__SGB6693	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Bacteroidota	c__Bacteroidia	o__Bacteroidales	f__Prevotellaceae	g__Prevotella	s__Prevotella_nanceiensis	t__SGB1536	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Clostridia	o__Eubacteriales	f__Eubacteriales_Family_XIII_Incertae_Sedis	g__Eubacteriales_Family_XIII_Incertae_Sedis_unclassified	s__Eubacterium_sulci	t__SGB3934_group	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Proteobacteria	c__Gammaproteobacteria	o__Pasteurellales	f__Pasteurellaceae	g__Haemophilus	s__Haemophilus_pittmaniae	t__SGB9656	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Bacilli	o__Lactobacillales	f__Carnobacteriaceae	g__Granulicatella	s__Granulicatella_SGB8255	t__SGB8255_group	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Bacilli	o__Bacillales	f__Bacillales_unclassified	g__Gemella	s__Gemella_haemolysans	t__SGB7292	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Bacilli	o__Lactobacillales	f__Streptococcaceae	g__Streptococcus	s__Streptococcus_urinalis	t__SGB8215	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Clostridia	o__Eubacteriales	f__Peptostreptococcaceae	g__Peptostreptococcus	s__Peptostreptococcus_SGB749	t__SGB749	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Actinomycetia	o__Actinomycetales	f__Actinomycetaceae	g__Varibaculum	s__Varibaculum_cambriense	t__SGB15481	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Bacilli	o__Lactobacillales	f__Streptococcaceae	g__Streptococcus	s__Streptococcus_sanguinis	t__SGB8047_group	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Bacteroidota	c__Bacteroidia	o__Bacteroidales	f__Prevotellaceae	g__Prevotella	s__Prevotella_sp_DNF00663	t__SGB3322	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Actinobacteria	c__Actinomycetia	o__Actinomycetales	f__Actinomycetaceae	g__Mobiluncus	s__Mobiluncus_SGB15489	t__SGB15489	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Tissierellia	o__Tissierellales	f__Peptoniphilaceae	g__Anaerococcus	s__Anaerococcus_SGB6672	t__SGB6672	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Fusobacteria	c__Fusobacteriia	o__Fusobacteriales	f__Fusobacteriaceae	g__Fusobacterium	s__Fusobacterium_nucleatum	t__SGB6001	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Bacteroidota	c__Bacteroidia	o__Bacteroidales	f__Porphyromonadaceae	g__Porphyromonas	s__Porphyromonas_sp_HMSC065F10	t__SGB1990_group	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Clostridia	o__Eubacteriales	f__Eubacteriales_Family_XIII_Incertae_Sedis	g__Eubacteriales_Family_XIII_Incertae_Sedis_unclassified	s__Clostridiales_bacterium_S5_A14a	t__SGB3977	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Fusobacteria	c__Fusobacteriia	o__Fusobacteriales	f__Fusobacteriaceae	g__Fusobacterium	s__Fusobacterium_nucleatum	t__SGB6014	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Fusobacteria	c__Fusobacteriia	o__Fusobacteriales	f__Fusobacteriaceae	g__Fusobacterium	s__Fusobacterium_nucleatum	t__SGB6011	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Bacilli	o__Lactobacillales	f__Streptococcaceae	g__Streptococcus	s__Streptococcus_infantis	t__SGB8086	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Tissierellia	o__Tissierellales	f__Peptoniphilaceae	g__Peptoniphilus	s__Peptoniphilus_sp_Marseille_P3761	t__SGB29485	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0
k__Bacteria	p__Firmicutes	c__Tissierellia	o__Tissierellales	f__Peptoniphilaceae	g__Anaerococcus	s__Anaerococcus_mediterraneensis	t__SGB29507	strain	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0	0	0.0	0.0	0.0	0	0.0	0	0.0	0.0	0	0.0	0.0	0	0.0	0.0	0.0	0	0.0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0	0	0	0.0	0	0	0.0	0.0	0.0	0.0	0.0	0.0

# Step 3. Aggregate removed strains by higher levels
removed_all_lvls <- strains_to_remove %>%
  # pivot_longer(cols = where(is.double), names_to = "sample", values_to = "removed_abundance") %>%
  select(-level) %>%
  pivot_longer(
    cols = kingdom:strain,
    names_to = "level",
    values_to = "name"
  ) %>%
  nest(.by = c(level)) %>%
  mutate(
    data = purrr::map(
      data,
      ~ summarise(.x, across(where(is.double), ~ sum(.)), .by = c("name"))
    )
  ) %>%
  mutate(data = setNames(.[["data"]], .$level))

removed_all_lvls

# A tibble: 8 × 2
  level   data               
  <chr>   <named list>       
1 kingdom <tibble [2 × 94]>  
2 phylum  <tibble [8 × 94]>  
3 class   <tibble [16 × 94]> 
4 order   <tibble [26 × 94]> 
5 family  <tibble [43 × 94]> 
6 genus   <tibble [74 × 94]> 
7 species <tibble [154 × 94]>
8 strain  <tibble [164 × 94]>

knitr::kable(removed_all_lvls$data[[2]], digits = 1)

name	KX63	KX64	S01	S02	S03	S04	S05	S06	S07	S08	S09	S10	S11	S12	S13	S14	S15	S16	S17	S18	S19	S20	S21	S22	S23	S24	S25	S26	S27	S28	S29	S30	S31	S32	S33	S34	S35	S36	S37	S38	S39	S40	S41	S42	S43	S44	S45	S46	S47	S48	S49	S50	S51	S52	S53	S54	S55	S56	S57	S58	S59	S60	S61	S62	S63_BL	S64_BL	S65_BL	S66_BL	S67_BL	S68_BL	S69_BL	S70_BL	S71_BL	S72_BL	S73_BL	S74_BL	S75_BL	S76_BL	S77_BL	S78_BL	S79_BL	S80_BL	S81_BL	S82_BL	S83_BL	S84_BL	S85_BL	S86_BL	S87_BL	S88_BL	S89_BL	S90_BL	S91_BL
p__Firmicutes	0	0.1	0	0.8	0.1	0	0.0	0	0	0	0	0	0	0	0	0.4	0	0	0.0	0	0	2.0	0	0	0	0.1	0.8	0	0.4	0	0	0.0	0	0.0	0	0	0.0	0	0	0.0	0.3	0	0	0	0	0.0	0	0.0	0.0	0	0	0	0	0.1	0	0	0	0	0	0	0	0.0	0.0	0.1	0	0.0	0	0	0.0	0	0.2	0	0	0	0	0	0	0	0	0	0.2	0	0	0	0	3.2	0.3	0.2	0.4	0	0.4	1.0	0
p__Actinobacteria	0	0.0	0	0.0	0.0	0	0.2	0	0	0	0	0	0	0	0	0.0	0	0	0.1	0	0	0.4	0	0	0	1.3	0.0	0	0.0	0	0	0.0	0	0.1	0	0	0.1	0	0	0.1	1.3	0	0	0	0	0.9	0	2.2	0.0	0	0	0	0	0.0	0	0	0	0	0	0	0	0.0	0.2	0.0	0	0.2	0	0	0.4	0	0.0	0	0	0	0	0	0	0	0	0	0.1	0	0	0	0	0.7	0.0	0.0	0.0	0	0.0	0.1	0
p__Bacteroidota	0	0.0	0	0.0	0.0	0	0.0	0	0	0	0	0	0	0	0	0.1	0	0	0.0	0	0	0.3	0	0	0	0.0	0.0	0	0.0	0	0	0.0	0	0.0	0	0	1.0	0	0	0.2	0.8	0	0	0	0	0.0	0	0.0	0.0	0	0	0	0	0.0	0	0	0	0	0	0	0	0.2	0.0	0.1	0	0.0	0	0	0.0	0	0.0	0	0	0	0	0	0	0	0	0	0.0	0	0	0	0	1.7	0.0	0.0	0.0	0	0.0	0.0	0
p__Tenericutes	0	0.0	0	0.0	0.0	0	0.0	0	0	0	0	0	0	0	0	0.0	0	0	0.0	0	0	0.0	0	0	0	0.0	0.0	0	0.0	0	0	0.0	0	0.0	0	0	0.0	0	0	0.0	0.0	0	0	0	0	0.0	0	0.0	0.0	0	0	0	0	0.0	0	0	0	0	0	0	0	0.0	0.0	0.0	0	0.0	0	0	0.0	0	0.0	0	0	0	0	0	0	0	0	0	0.0	0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0
p__Proteobacteria	0	0.0	0	0.0	0.0	0	0.0	0	0	0	0	0	0	0	0	0.0	0	0	0.0	0	0	0.0	0	0	0	0.0	0.0	0	0.0	0	0	0.0	0	0.0	0	0	0.0	0	0	0.0	0.0	0	0	0	0	0.0	0	0.0	0.0	0	0	0	0	0.0	0	0	0	0	0	0	0	0.0	0.5	0.0	0	0.0	0	0	0.0	0	0.0	0	0	0	0	0	0	0	0	0	0.0	0	0	0	0	0.3	0.0	0.0	0.0	0	0.1	0.0	0
p__Ascomycota	0	0.0	0	0.0	0.0	0	0.0	0	0	0	0	0	0	0	0	0.0	0	0	0.0	0	0	0.0	0	0	0	0.0	0.0	0	0.0	0	0	1.1	0	0.0	0	0	0.0	0	0	0.0	0.0	0	0	0	0	0.0	0	0.0	0.1	0	0	0	0	0.0	0	0	0	0	0	0	0	0.0	0.0	0.0	0	0.0	0	0	0.0	0	0.0	0	0	0	0	0	0	0	0	0	0.0	0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0
p__Synergistetes	0	0.0	0	0.0	0.0	0	0.0	0	0	0	0	0	0	0	0	0.0	0	0	0.0	0	0	0.0	0	0	0	0.0	0.0	0	0.0	0	0	0.0	0	0.0	0	0	0.0	0	0	0.0	0.0	0	0	0	0	0.0	0	0.0	0.0	0	0	0	0	0.0	0	0	0	0	0	0	0	0.0	0.0	0.0	0	0.0	0	0	0.0	0	0.0	0	0	0	0	0	0	0	0	0	0.0	0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0
p__Fusobacteria	0	0.0	0	0.0	0.0	0	0.0	0	0	0	0	0	0	0	0	0.0	0	0	0.0	0	0	0.0	0	0	0	0.0	0.0	0	0.0	0	0	0.0	0	0.0	0	0	0.0	0	0	0.0	0.0	0	0	0	0	0.0	0	0.0	0.0	0	0	0	0	0.0	0	0	0	0	0	0	0	0.0	0.0	0.0	0	0.0	0	0	0.0	0	0.0	0	0	0	0	0	0	0	0	0	0.0	0	0	0	0	0.0	0.0	0.0	0.0	0	0.0	0.0	0

# Step 4. get longer format and add back clade_names
# function to get clade name
get_full_clade.fun <- function(df) {
  # This will add a new column called match_clade
  # with the full clade_name that ends with the string from tissue_renorm_filt$clade_name
  df %>%
    mutate(
      match_clade = map_chr(
        name,
        ~ {
          hit <- data$clade_name[str_detect(
            data$clade_name,
            paste0(.x, "$")
          )]
          if (length(hit) > 0) hit[1] else NA_character_
        }
      )
    ) %>%
    select(match_clade) %>%
    pull()
}

removals <- removed_all_lvls %>%
  unnest(cols = data) %>%
  mutate(clade_name = get_full_clade.fun(.))

#############################
# FILTER AT ALL TAXA LEVELS #
############################
# Step 5. Subtract from higher levels
data_filt <- data %>%
  # Join percentages to be subtracted
  left_join(
    select(removals, -name, -level),
    by = "clade_name",
    suffix = c("", "_rm")
  ) %>%
  # Subtract sample-wise values
  mutate(
    across(
      matches("^S\\d\\d$"),
      ~ .x - coalesce(get(paste0(cur_column(), "_rm")), 0)
    )
  ) %>%
  select(-ends_with("_rm"))

# --- Step 6: check and replace negatives ---
indx <- which(data_filt < 0, arr.ind = TRUE)

Warning in Ops.factor(left, right): '<' not meaningful for factors

if (nrow(indx) > 0) {
  neg_report <- tibble(
    neg    = map2_dbl(indx[,1], indx[,2], ~ data_filt[[.x, .y]]),
    remove = map2_dbl(indx[,1], indx[,2], ~ data[[.x, .y]]),  # original value from data
    col    = map_chr(indx[,2], ~ colnames(data)[.x]),         # column name
    tax    = map_chr(indx[,1], ~ data[[.x, 1]])               # taxon/clade name
  )
  
  message("Negative values found and replaced with 0:")
  print(neg_report)

  # --- Step 7: replace negatives with zero ---
  data_filt <- data_filt %>%
  mutate(across(where(is.numeric), ~ pmax(.x, 0)))
}

Negative values found and replaced with 0:

# A tibble: 2 × 4
         neg remove col   tax                                                   
       <dbl>  <dbl> <chr> <chr>                                                 
1 -0.0000100 0.0147 S54   k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissiere…
2 -0.0000100 0.145  S61   k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Cor…

# test
strains_to_remove %>% pull("S39") %>% sum(.)

[1] 2.42705

data_filt %>% filter(level == "genus") %>% pull("S39") %>% sum(.)

[1] 97.57293

#####################################
# RENORMALIZED FILTERED TAXA VALUES #
#####################################
# Step 6. Re-normalize so each sample sums to 100
data_filt_norm <- data_filt %>%
  group_by(level) %>%
  mutate(
    across(
      matches("^S\\d\\d$"),
      ~ .x * 100 / sum(.x, na.rm = TRUE)
    )
  ) %>%
  ungroup()

# test
data_filt_norm %>% filter(level == "genus") %>% pull("S39") %>% sum(.)

[1] 100

Save filtered table

data_filt_norm %>%
  #select(-Pos_Seq_Ctrl) %>%
  arrange(level) %>%
  write_csv(
    .,
    "../Results/MixOmic/Metageonome_all_vagswab_metaphlan_taxa_filt.csv"
  )
# data_filt_norm <- read_csv("../Results/Tissue_QC/Metageonome_all_vagswab_metaphlan_taxa_filt.csv")

Step 3: Centered Log Ratio (CLR) Transformation

For technical, biological and computational reasons, microbiome data is compositional such that they represent proportions or relative information. Proportional data are restricted to a space where the sum of all OTU proportions for a given sample sums to 1. Using standard statistical methods on such data may lead to spurious results. Likewise, any data that are compositional in nature are interpreted into relative counts. Hence, using a CLR transformation allows the circumvention of these spurious results.

There are two ways of log-ratio transforming the data in mixOmics:

Option 1: Some of our functions (pca, plsda) directly include the argument logratio = 'CLR', so all you need to do is include your filtered offset data and add this argument (see example below).
Option 2: Some functions currently do not include the logratio argument. In this case, you will need to use the logratio.transfo() function as shown below. You can also use this function if you only have access to TSS (proportions) data and those were not offset.

unlike 16S data which are returned as raw counts after pre-processing, shotgun metageome data is often already normalized into proportions. This is because direct counts aren’t very meaningful across different taxa/genomes. That is why we will go with option 2 for our data.

🔹 Shotgun metagenomics

• You sequence all DNA in the sample, not just one marker gene.
  
• Reads are mapped to reference genomes, genes, or functional categories.
  
• Raw counts can be biased by factors like:
  • genome size
    
  • gene length
    
  • variable sequencing depth
    
• Because of this, many sequencing facilities preprocess shotgun data to produce normalized relative abundances (proportions), so that samples can be compared more easily.

Typical outputs include:
- Relative abundance (%) of taxa
- RPKM / TPM / CPM for genes or functions

gr <- tibble(ID = colnames(data)[-c(1,2)]) %>% 
    left_join(., gr_data, by =c("ID"="svamp_ID")) %>%
    mutate(
      pos = case_when(
        `Fungal culture: C. albicans (y/n)` == "1" |
        `Fungal culture: Non-albicans candida spp. (y/n)` == 1 ~
        "pos",
        TRUE ~ "neg"
        ), .after="group")

Now we want to simplify the clade_name column so that:

• For phylum / class / order / family / genus, only the relevant level is kept.
• For species and strain, all levels are incuded down from genus,
  i.e. "Genus species" or "Genus species strain".

# string manipulation

# data_filt_norm <- read_csv("../Results/Tissue_QC/Metageonome_all_vagswab_metaphlan_taxa_filt.csv")

# Modify taxa labels 
data_filt_norm <- data_filt_norm %>%
  mutate(
    taxa = str_extract_all(clade_name, "(?<=k__|p__|c__|o__|f__|g__|s__|t__)[^|]+"),
    taxa = map2_chr(taxa, level, ~ {
      if (.y %in% c("species", "strain")) {
        # keep everything from genus onward
        start <- which(c("k","p","c","o","f","g","s","t") %in% substr(.y,1,1))
        paste(.x[start:length(.x)], collapse = " ")
      } else {
        # keep only the last element (current level)
        tail(.x, 1)
      }
    }),
    .after = "level"
  ) %>%
  select(-clade_name) %>%
  rename(clade_name = taxa)

# Create matrix for all levels of taxa
# NB! the majority(?) of mixOmics functions expect a format of
# samples as rows and features as columns, thus the transformation 
# is VERY important!
matrix <- data_filt_norm %>%
    #rename_with(~ str_replace(.x, "_BL$", ""), everything()) %>%
    nest(data = -level) %>%
    # filter(level == "strain") %>%
    mutate(
    data = map(
      data,
      ~ .x %>%
        column_to_rownames(var = "clade_name") %>%
        as.matrix() %>%
        t()
    )
  )

matrix

# A tibble: 8 × 2
  level   data            
  <fct>   <list>          
1 kingdom <dbl [93 × 2]>  
2 phylum  <dbl [93 × 10]> 
3 class   <dbl [93 × 20]> 
4 order   <dbl [93 × 31]> 
5 family  <dbl [93 × 56]> 
6 genus   <dbl [93 × 99]> 
7 species <dbl [93 × 220]>
8 strain  <dbl [93 × 244]>

# Specify levels you want to process
tax_levels <- c("order", "family", "genus", "species", "strain")


matrix <- matrix %>%
  # Apply CLR transformation and PCA to each level
  mutate(
    clr_data = map(data, ~ logratio.transfo(.x, logratio = "CLR", offset = 1))
  ) %>%
    mutate(across(2:3, ~set_names(.x, paste0(.data[["level"]]))))

write_csv(
  matrix,
  "../Results/MixOmic/Metageonome_vagswab_CLR_transformed.csv"
)
# matrix <- read_csv("../Results/MixOmic/Metageonome_vagswab_CLR_transformed.csv")

matrix <- matrix %>%
  # Filter matrix to only these levels
  filter(level %in% tax_levels) %>%
  
  # Apply CLR transformation and PCA to each level
  mutate(
    #clr_data = map(data, ~ logratio.transfo(.x, logratio = "CLR", offset = 1)),
    pca_res  = map(clr_data, ~ pca(.x)),
    plot = map2(pca_res, level, ~plotIndiv(.x, 
                group = gr$pos, ind.names = F, size.title = 9,
                title = paste0(.y))),
    plot2 = map2(pca_res, level, ~plotIndiv(.x, 
                group = gr$group, ind.names = F, size.title = 9,
                title = paste0(.y)))
  ) %>%
    mutate(across(2:5, ~set_names(.x, paste0(.data[["level"]]))))

# Plot PCA for selected levels
l <- get_legend(plotIndiv(matrix$pca_res[["genus"]], legend = T, group = gr$pos)$graph)

l2 <- get_legend(plotIndiv(matrix$pca_res[["genus"]], legend = T, group = gr$group)$graph)

p <- matrix$plot %>% map("graph")
p2 <- matrix$plot2 %>% map("graph")
plot_grid(
  plotlist = c(list(l),p),
  #labels = matrix$level,   # use taxonomy levels as labels
  ncol = 3
)

plot_grid(
  plotlist = c(list(l2),p2),
  #labels = matrix$level,   # use taxonomy levels as labels
  ncol = 3
)

There are no clear seperation between the labels at any of the taxa levels. A google search indicate that Some studies find family or genus level is often most informative. Im wondering weather I can combine the matrix for genus and species level and to the PLS-DA on that?

Now that the data is:

• filtered for low abundant taxa
  
• CLR transformed
  
• offset added

Now we can move on to the Feature selection (PLS-DA) For this portion of the script we are following the MixOmics tutorial here: https://mixomics.org/mixmc/koren-bodysites-case-study/

Feature selection

We want to do use a Multivariate feature selection method (PLS-DA). Multivariate methods considers features collectively, accounting for their interplay and redundancy, aiming for “more accurate prediction”

# combined genus and species levels with neg and pos only
m <- cbind(matrix$clr_data$genus, matrix$clr_data$species)
g <- gr$pos

# genus only and withouth samples with NA values 
#m <- matrix$clr_data$genus[!is.na(gr$group),]
#g <- gr$group[!is.na(gr$group)]

basic.plsda = plsda(m, g, logratio = 'none', 
                          ncomp = 3)

# assess the performance of the sPLS-DA model using repeated CV
perf.plsda = perf(basic.plsda,  
                  validation = 'Mfold', 
                  folds = 5, nrepeat = 10, 
                  progressBar = FALSE)

# extract the optimal component number
optimal.ncomp <- perf.plsda$choice.ncomp["BER", "max.dist"] 

plot(perf.plsda, overlay = 'measure', sd=TRUE) # plot this tuning

Tuning of the model

grid.keepX = c(seq(5,150, 5))

tune.splsda = tune.splsda(m, gr$pos, 
                          ncomp = optimal.ncomp, # use optimal component number
                          logratio = 'none', # transform data to euclidean space
                          test.keepX = grid.keepX,
                          validation = c('Mfold'),
                          folds = 5, nrepeat = 10, # use repeated CV
                          dist = 'max.dist', # maximum distance as metric
                          progressBar = FALSE)

# extract the optimal component number and optimal feature count per component
optimal.keepX = tune.splsda$choice.keepX[1:2] 
optimal.ncomp = tune.splsda$choice.ncomp$ncomp 

plot(tune.splsda) # plot this tuning

For each component (coloured according to the legend), the optimal number of features to select is shown by the large diamonds. This is selected per component using a one-sided t-test. The y-axis depicts the average correlation between the predicted and actual components. This is cross-validated over folds folds and repeated nrepeat times.

optimised model

splsd.mod = splsda(m, gr$pos, logratio= "none", # form final sPLS-DA model
                ncomp = 2, 
                keepX = optimal.keepX)

plotIndiv(splsd.mod,
          comp = c(1,2),
          ind.names = FALSE,
          ellipse = TRUE, # include confidence ellipses
          legend = TRUE, size.title = 9,
          legend.title = "Candida",
          title = 'sPLS-DA Comps 1&2')

png("cim_plot.png", width = 2000, height = 2000, res = 300)
cim(splsd.mod,
    comp = c(1,2),
    margins = c(10, 5),
    row.sideColors = color.mixo(factor(gr$pos)), # row colors by bodysite
    legend = list(legend = levels(factor(gr$pos))),
    title = 'Clustered Image Map of Koren Bodysite data')
dev.off()

quartz_off_screen 
                2 

plotVar(splsd.mod,
        comp = c(1,2),
        cutoff = 0.7, rad.in = 0.7,
        title = 'Correlation Circle Plot Comps 1&2')

png("network_plot_.png", width = 6.7, height = 6.7, res = 300, units = "in")
network(splsd.mod,
        size.node = 0.05, cex.node.name = 0.5,
        cutoff = 0.1, block.var.names = F, plot.graph = FALSE,
        color.node = c("orange","lightblue"))

dev.off()

quartz_off_screen 
                3 

evaluate PLS-DA

# evaluate classification, using repeated CV and maximum distance as metric
perf.splsda = perf(splsd.mod, validation = 'Mfold', 
                         folds = 5, nrepeat = 10, 
                         progressBar = FALSE, dist = 'max.dist') 

perf.splsda$error.rate

$overall
       max.dist
comp1 0.3258065
comp2 0.2989247

$BER
       max.dist
comp1 0.3229417
comp2 0.2966004

Taxa selection

par( mfrow= c(1,2) )
p <- map(c(1,2), ~plotLoadings(splsd.mod, comp = .x, 
             method = 'mean', contrib = 'max',  
             size.name = 0.8, legend = FALSE, size.title = 1,
             ndisplay = 20, style = "ggplot2",
             title = paste0("Loadings of Component ",.x)) )

'ndisplay' value is larger than the number of selected variables! It has been reseted to 5 for block X

# determine which OTUs were selected
selected.OTU.comp1 = selectVar(splsd.mod, comp = 1)$name 
selected.OTU.comp2 = selectVar(splsd.mod, comp = 2)$name 

# display the stability values of these OTUs
perf.splsda$features$stable[[1]][selected.OTU.comp1] 

        Candida_albicans                Dialister Dialister_micraerophilus 
                    1.00                     0.96                     0.88 
             Megasphaera                   GGB754 
                    0.48                     0.30 

perf.splsda$features$stable[[2]][selected.OTU.comp2] 

                        Megasphaera                  Megasphaera_lornae 
                               0.94                                0.94 
                            GGB3012                     GGB3012_SGB4003 
                               0.94                                0.94 
                             GGB753    Limosilactobacillus_coleohominis 
                               0.94                                0.96 
                      GGB753_SGB989              Lactobacillus_jensenii 
                               0.94                                0.94 
                      GGB754_SGB990              Lancefieldella_parvula 
                               0.86                                0.92 
      Coriobacteriales_unclassified Coriobacteriales_bacterium_DNF00809 
                               0.88                                0.88 
           Streptococcus_agalactiae    Corynebacterium_glucuronolyticum 
                               0.92                                0.88 
                     Lancefieldella                              GGB754 
                               0.92                                0.82 
              Porphyromonas_uenonis                       Porphyromonas 
                               0.92                                0.90 
                     Staphylococcus                       Streptococcus 
                               0.88                                0.88 
      Limosilactobacillus_vaginalis            Anaerococcus_jeddahensis 
                               0.82                                0.86 
              Staphylococcus_aureus           Tissierellia_unclassified 
                               0.86                                0.82 
                    Corynebacterium        Lacticaseibacillus_paracasei 
                               0.86                                0.86 
                Prevotella_corporis                   Peptococcus_niger 
                               0.88                                0.88 
            Peptoniphilus_duerdenii            Haemophilus_haemolyticus 
                               0.88                                0.88 
     Tissierellia_bacterium_KA00581             Peptoniphilus_gorbachii 
                               0.84                                0.88 
                    GGB1144_SGB1468                         Gardnerella 
                               0.88                                0.82 
          Anaerococcus_hydrogenalis               Gardnerella_vaginalis 
                               0.80                                0.82 
                   Prevotella_amnii                             GGB1144 
                               0.78                                0.82 
                           Sneathia                         Haemophilus 
                               0.78                                0.82 
                Veillonella_atypica                Actinomyces_SGB17132 
                               0.78                                0.82 
                        Peptococcus                           Atopobium 
                               0.82                                0.80 
                Prevotella_buccalis                  Peptostreptococcus 
                               0.80                                0.94 
               Prevotella_veroralis                             Gemella 
                               0.88                                0.78 
  Corynebacterium_pyruviciproducens                  Sneathia_vaginalis 
                               0.80                                0.70 
                Schaalia_turicensis                Prevotella_bergensis 
                               0.78                                0.78 
               Prevotella_denticola                      Slackia_exigua 
                               0.86                                0.78 
                Streptococcus_mitis                 Peptoniphilus_coxii 
                               0.76                                0.80 
                   Escherichia_coli                         Actinomyces 
                               0.76                                0.72 
          Anaerococcus_lactolyticus                   GGB73389_SGB46635 
                               0.74                                0.70 
                         Finegoldia                            GGB73389 
                               0.72                                0.82 
      Peptostreptococcus_anaerobius                 Salmonella_enterica 
                               0.82                                0.76 
                           Schaalia                    Atopobium_deltae 
                               0.72                                0.74 
            Lactobacillus_crispatus                    Parvimonas_parva 
                               0.68                                0.76 
              Prevotella_vespertina                  Prevotella_pallens 
                               0.74                                0.72 
                            Slackia                 Peptoniphilus_harei 
                               0.72                                0.68 
              Anaerococcus_prevotii                         Escherichia 
                               0.72                                0.70 
                    GGB1460_SGB2023                   Prevotella_jejuni 
                               0.68                                0.68 
                             Winkia              Listeria_monocytogenes 
                               0.54                                0.66 
                   GGB36599_SGB9269               Lactobacillus_gasseri 
                               0.66                                0.58 
             Pseudomonas_aeruginosa              Varibaculum_cambriense 
                               0.66                                0.66 
                         Salmonella                   Atopobium_minutum 
                               0.64                                0.62 
             Anaerococcus_vaginalis                  Neisseria_subflava 
                               0.58                                0.64 
                         Parvimonas            Urinicoccus_massiliensis 
                               0.64                                0.58 
         Haemophilus_parainfluenzae                        Anaerococcus 
                               0.58                                0.54 
             Actinotignum_timonense                    Finegoldia_magna 
                               0.58                                0.64 
     Mannheimia_massilioguelmaensis         Streptococcus_parasanguinis 
                               0.58                                0.58 
                Lactobacillus_iners                             GGB1460 
                               0.50                                0.56 
            Gemella_asaccharolytica                            GGB36599 
                               0.62                                0.54 
                           Listeria                         Pseudomonas 
                               0.56                                0.56 
                        Varibaculum                         Urinicoccus 
                               0.54                                0.54 
                          Neisseria                        Actinotignum 
                               0.54                                0.56 
               Streptococcus_oralis                          Mannheimia 
                               0.50                                0.56 
        Megasphaera_micronuciformis                  Actinomyces_sp_ph3 
                               0.58                                0.58 
                      Lactobacillus                Prevotella_histicola 
                               0.68                                0.56 
              Levyella_massiliensis              Streptococcus_gordonii 
                               0.42                                0.56 
                 Bulleidia_extructa                 Rothia_mucilaginosa 
                               0.56                                0.50 
                Cutibacterium_acnes                 Veillonella_parvula 
                               0.46                                0.50 
                 Veillonella_dispar              Dialister_pneumosintes 
                               0.48                                0.44 
         Senegalimassilia_anaerobia                      Granulicatella 
                               0.44                                0.52 
                       Winkia_neuii                       Cutibacterium 
                               0.50                                0.56 
     Clostridium_massiliamazoniense            Alloscardovia_omnicolens 
                               0.40                                0.62 
                    GGB4260_SGB5794                            Levyella 
                               0.44                                0.48 
                          Bulleidia           Anaerococcus_senegalensis 
                               0.50                                0.44 
                      Solobacterium               Prevotella_nigrescens 
                               0.50                                0.44 
          Streptococcus_intermedius                              Rothia 
                               0.44                                0.52 
             Anaerococcus_tetradius                 Veillonella_rogosae 
                               0.50                                0.42 
                   Senegalimassilia              Bifidobacterium_longum 
                               0.50                                0.42 
                        Clostridium                     GGB1144_SGB1469 
                               0.52                                0.42 
                    Prevotella_oris                             GGB4260 
                               0.44                                0.50 
           Streptococcus_salivarius               Solobacterium_SGB6829 
                               0.44                                0.44 
             Granulicatella_SGB8239              Mogibacterium_diversum 
                               0.44                                0.44 
            Granulicatella_adiacens           Peptostreptococcus_sp_MV1 
                               0.44                                0.44 
                      Mogibacterium             Streptococcus_australis 
                               0.50                                0.44 
         Streptococcus_constellatus                       Fusobacterium 
                               0.44                                0.50